1 #ifndef SINGLEQMODEL_H_
2 #define SINGLEQMODEL_H_
13 #include "my_assert.h"
14 #include "Orientation.h"
19 #include "NoiseQProfile.h"
21 #include "ModelParams.h"
24 #include "SingleReadQ.h"
25 #include "SingleHit.h"
26 #include "ReadReader.h"
32 SingleQModel(Refs* refs = NULL) {
34 M = (refs != NULL ? refs->getM() : 0);
35 memset(N, 0, sizeof(N));
37 needCalcConPrb = true;
39 ori = new Orientation();
42 rspd = new RSPD(estRSPD);
44 qpro = new QProfile();
45 nqpro = new NoiseQProfile();
47 mean = -1.0; sd = 0.0;
53 //If it is not a master node, only init & update can be used!
54 SingleQModel(ModelParams& params, bool isMaster = true) {
56 memcpy(N, params.N, sizeof(params.N));
58 estRSPD = params.estRSPD;
59 mean = params.mean; sd = params.sd;
60 seedLen = params.seedLen;
61 needCalcConPrb = true;
63 ori = NULL; gld = NULL; mld = NULL; rspd = NULL; qd = NULL; qpro = NULL; nqpro = NULL;
67 gld = new LenDist(params.minL, params.maxL);
68 if (mean >= EPSILON) {
69 mld = new LenDist(params.mate_minL, params.mate_maxL);
71 if (!estRSPD) { rspd = new RSPD(estRSPD); }
75 ori = new Orientation(params.probF);
76 if (estRSPD) { rspd = new RSPD(estRSPD, params.B); }
77 qpro = new QProfile();
78 nqpro = new NoiseQProfile();
83 if (ori != NULL) delete ori;
84 if (gld != NULL) delete gld;
85 if (mld != NULL) delete mld;
86 if (rspd != NULL) delete rspd;
87 if (qd != NULL) delete qd;
88 if (qpro != NULL) delete qpro;
89 if (nqpro != NULL) delete nqpro;
90 if (mw != NULL) delete[] mw;
94 //SingleQModel& operator=(const SingleQModel&);
96 void estimateFromReads(const char*);
98 //if prob is too small, just make it 0
99 double getConPrb(const SingleReadQ& read, const SingleHit& hit) const {
100 if (read.isLowQuality()) return 0.0;
103 int sid = hit.getSid();
104 RefSeq &ref = refs->getRef(sid);
105 int fullLen = ref.getFullLen();
106 int totLen = ref.getTotLen();
107 int dir = hit.getDir();
108 int pos = hit.getPos();
109 int readLen = read.getReadLength();
110 int fpos = (dir == 0 ? pos : totLen - pos - readLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
112 general_assert(fpos >= 0, "The alignment of read " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
113 " from the forward direction, which should be a non-negative number! " + \
114 "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
115 general_assert(fpos + readLen <= totLen,"Read " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
116 + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
117 general_assert(readLen <= totLen, "Read " + read.getName() + " has length " + itos(readLen) + ", but it is aligned to transcript " \
118 + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the read's length!");
120 int seedPos = (dir == 0 ? pos : totLen - pos - seedLen); // the aligned position of the seed in forward strand coordinates
121 if (seedPos >= fullLen || ref.getMask(seedPos)) return 0.0;
127 int minL = std::max(readLen, gld->getMinL());
128 int maxL = std::min(totLen - pos, gld->getMaxL());
129 int pfpos; // possible fpos for fragment
131 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
132 pfpos = (dir == 0 ? pos : totLen - pos - fragLen);
133 effL = std::min(fullLen, totLen - fragLen + 1);
134 value += gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen) * mld->getAdjustedProb(readLen, fragLen);
138 effL = std::min(fullLen, totLen - readLen + 1);
139 value = gld->getAdjustedProb(readLen, totLen) * rspd->getAdjustedProb(fpos, effL, fullLen);
142 prob = ori->getProb(dir) * value * qpro->getProb(read.getReadSeq(), read.getQScore(), ref, pos, dir);
144 if (prob < EPSILON) { prob = 0.0; }
146 prob = (mw[sid] < EPSILON ? 0.0 : prob / mw[sid]);
151 double getNoiseConPrb(const SingleReadQ& read) {
152 if (read.isLowQuality()) return 0.0;
153 double prob = mld != NULL ? mld->getProb(read.getReadLength()) : gld->getProb(read.getReadLength());
154 prob *= nqpro->getProb(read.getReadSeq(), read.getQScore());
155 if (prob < EPSILON) { prob = 0.0; }
157 prob = (mw[0] < EPSILON ? 0.0 : prob / mw[0]);
162 double getLogP() { return nqpro->getLogP(); }
166 void update(const SingleReadQ& read, const SingleHit& hit, double frac) {
167 if (read.isLowQuality() || frac < EPSILON) return;
169 const RefSeq& ref = refs->getRef(hit.getSid());
171 int dir = hit.getDir();
172 int pos = hit.getPos();
175 int fullLen = ref.getFullLen();
177 // Only use one strand to estimate RSPD
178 if (ori->getProb(0) >= ORIVALVE && dir == 0) {
179 rspd->update(pos, fullLen, frac);
182 if (ori->getProb(0) < ORIVALVE && dir == 1) {
183 int totLen = ref.getTotLen();
184 int readLen = read.getReadLength();
189 int minL = std::max(readLen, gld->getMinL());
190 int maxL = std::min(totLen - pos, gld->getMaxL());
192 assert(maxL >= minL);
193 std::vector<double> frag_vec(maxL - minL + 1, 0.0);
195 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
196 pfpos = totLen - pos - fragLen;
197 effL = std::min(fullLen, totLen - fragLen + 1);
198 frag_vec[fragLen - minL] = gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen) * mld->getAdjustedProb(readLen, fragLen);
199 sum += frag_vec[fragLen - minL];
201 assert(sum >= EPSILON);
202 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
203 pfpos = totLen - pos - fragLen;
204 rspd->update(pfpos, fullLen, frac * (frag_vec[fragLen - minL] / sum));
208 rspd->update(totLen - pos - readLen, fullLen, frac);
212 qpro->update(read.getReadSeq(), read.getQScore(), ref, pos, dir, frac);
215 void updateNoise(const SingleReadQ& read, double frac) {
216 if (read.isLowQuality() || frac < EPSILON) return;
218 nqpro->update(read.getReadSeq(), read.getQScore(), frac);
223 void collect(const SingleQModel&);
225 //void copy(const SingleQModel&);
227 bool getNeedCalcConPrb() { return needCalcConPrb; }
228 void setNeedCalcConPrb(bool value) { needCalcConPrb = value; }
232 //double* getP1() { return p1; }
233 //double* getP2() { return p2; }
235 void read(const char*);
236 void write(const char*);
238 const LenDist& getGLD() { return *gld; }
240 void startSimulation(simul*, double*);
241 bool simulate(int, SingleReadQ&, int&);
242 void finishSimulation();
244 //Use it after function 'read' or 'estimateFromReads'
250 int getModelType() const { return model_type; }
253 static const int model_type = 1;
254 static const int read_type = 1;
261 //double *p1, *p2; P_i' & P_i'';
263 bool estRSPD; // true if estimate RSPD
264 bool needCalcConPrb; //true need, false does not need
271 NoiseQProfile *nqpro;
273 simul *sampler; // for simulation
274 double *theta_cdf; // for simulation
276 double *mw; // for masking
281 void SingleQModel::estimateFromReads(const char* readFN) {
283 char readFs[2][STRLEN];
286 mld != NULL ? mld->init() : gld->init();
287 for (int i = 0; i < 3; i++)
289 genReadFileNames(readFN, i, read_type, s, readFs);
290 ReadReader<SingleReadQ> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function
293 while (reader.next(read)) {
294 if (!read.isLowQuality()) {
295 mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
296 qd->update(read.getQScore());
297 if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
299 else if (verbose && read.getReadLength() < seedLen) {
300 printf("Warning: Read %s is ignored due to read length %d < seed length %d!\n", read.getName().c_str(), read.getReadLength(), seedLen);
304 if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
307 if (verbose) { printf("estimateFromReads, N%d finished.\n", i); }
310 mld != NULL ? mld->finish() : gld->finish();
313 if (mean >= EPSILON) {
314 assert(mld->getMaxL() <= gld->getMaxL());
315 gld->setAsNormal(mean, sd, std::max(mld->getMinL(), gld->getMinL()), gld->getMaxL());
318 nqpro->calcInitParams();
320 mw = new double[M + 1];
324 void SingleQModel::init() {
325 if (estRSPD) rspd->init();
330 void SingleQModel::finish() {
331 if (estRSPD) rspd->finish();
334 needCalcConPrb = true;
335 if (estRSPD) calcMW();
338 void SingleQModel::collect(const SingleQModel& o) {
339 if (estRSPD) rspd->collect(*(o.rspd));
340 qpro->collect(*(o.qpro));
341 nqpro->collect(*(o.nqpro));
344 //Only master node can call
345 void SingleQModel::read(const char* inpF) {
347 FILE *fi = fopen(inpF, "r");
348 if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
350 assert(fscanf(fi, "%d", &val) == 1);
351 assert(val == model_type);
355 assert(fscanf(fi, "%d", &val) == 1);
357 if (mld == NULL) mld = new LenDist();
365 if (fscanf(fi, "%d", &val) == 1) {
368 mw = new double[M + 1];
369 for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
376 //Only master node can call. Only be called at EM.cpp
377 void SingleQModel::write(const char* outF) {
378 FILE *fo = fopen(outF, "w");
380 fprintf(fo, "%d\n", model_type);
383 ori->write(fo); fprintf(fo, "\n");
384 gld->write(fo); fprintf(fo, "\n");
389 else { fprintf(fo, "0\n"); }
391 rspd->write(fo); fprintf(fo, "\n");
392 qd->write(fo); fprintf(fo, "\n");
393 qpro->write(fo); fprintf(fo, "\n");
397 fprintf(fo, "\n%d\n", M);
398 for (int i = 0; i < M; i++) {
399 fprintf(fo, "%.15g ", mw[i]);
401 fprintf(fo, "%.15g\n", mw[M]);
407 void SingleQModel::startSimulation(simul* sampler, double* theta) {
408 this->sampler = sampler;
410 theta_cdf = new double[M + 1];
411 for (int i = 0; i <= M; i++) {
412 theta_cdf[i] = theta[i];
413 if (i > 0) theta_cdf[i] += theta_cdf[i - 1];
416 rspd->startSimulation(M, refs);
417 qd->startSimulation();
418 qpro->startSimulation();
419 nqpro->startSimulation();
422 bool SingleQModel::simulate(int rid, SingleReadQ& read, int& sid) {
423 int dir, pos, readLen, fragLen;
425 std::string qual, readseq;
426 std::ostringstream strout;
428 sid = sampler->sample(theta_cdf, M + 1);
432 readLen = (mld != NULL ? mld->simulate(sampler, -1) : gld->simulate(sampler, -1));
433 qual = qd->simulate(sampler, readLen);
434 readseq = nqpro->simulate(sampler, readLen, qual);
437 RefSeq &ref = refs->getRef(sid);
438 dir = ori->simulate(sampler);
439 fragLen = gld->simulate(sampler, ref.getTotLen());
440 if (fragLen < 0) return false;
442 int effL = std::min(ref.getFullLen(), ref.getTotLen() - fragLen + 1);
443 pos = rspd->simulate(sampler, sid, effL);
444 if (pos < 0) return false;
445 if (dir > 0) pos = ref.getTotLen() - pos - fragLen;
448 readLen = mld->simulate(sampler, fragLen);
449 if (readLen < 0) return false;
450 qual = qd->simulate(sampler, readLen);
451 readseq = qpro->simulate(sampler, readLen, pos, dir, qual, ref);
454 qual = qd->simulate(sampler, fragLen);
455 readseq = qpro->simulate(sampler, fragLen, pos, dir, qual, ref);
459 strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
462 read = SingleReadQ(name, readseq, qual);
467 void SingleQModel::finishSimulation() {
470 rspd->finishSimulation();
471 qd->finishSimulation();
472 qpro->finishSimulation();
473 nqpro->finishSimulation();
476 void SingleQModel::calcMW() {
479 assert((mld == NULL ? gld->getMinL() : mld->getMinL()) >= seedLen);
481 memset(mw, 0, sizeof(double) * (M + 1));
484 probF = ori->getProb(0);
485 probR = ori->getProb(1);
487 for (int i = 1; i <= M; i++) {
488 RefSeq& ref = refs->getRef(i);
489 int totLen = ref.getTotLen();
490 int fullLen = ref.getFullLen();
494 int end = std::min(fullLen, totLen - seedLen + 1);
497 for (int seedPos = 0; seedPos < end; seedPos++)
498 if (ref.getMask(seedPos)) {
500 minL = gld->getMinL();
501 maxL = std::min(gld->getMaxL(), totLen - seedPos);
503 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
504 effL = std::min(fullLen, totLen - fragLen + 1);
505 factor = (mld == NULL ? 1.0 : mld->getAdjustedCumulativeProb(std::min(mld->getMaxL(), fragLen), fragLen));
506 value += probF * gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen) * factor;
509 minL = gld->getMinL();
510 maxL = std::min(gld->getMaxL(), seedPos + seedLen);
511 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
512 pfpos = seedPos - (fragLen - seedLen);
513 effL = std::min(fullLen, totLen - fragLen + 1);
514 factor = (mld == NULL ? 1.0 : mld->getAdjustedCumulativeProb(std::min(mld->getMaxL(), fragLen), fragLen));
515 value += probR * gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen) * factor;
519 //for reverse strand masking
520 for (int seedPos = end; seedPos <= totLen - seedLen; seedPos++) {
521 minL = std::max(gld->getMinL(), seedPos + seedLen - fullLen + 1);
522 maxL = std::min(gld->getMaxL(), seedPos + seedLen);
523 for (int fragLen = minL; fragLen <= maxL; fragLen++) {
524 pfpos = seedPos - (fragLen - seedLen);
525 effL = std::min(fullLen, totLen - fragLen + 1);
526 factor = (mld == NULL ? 1.0 : mld->getAdjustedCumulativeProb(std::min(mld->getMaxL(), fragLen), fragLen));
527 value += probR * gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen) * factor;
534 // fprintf(stderr, "Warning: %dth reference sequence is masked for almost all positions!\n", i);
540 #endif /* SINGLEQMODEL_H_ */